Genetic Variant TNRC18:p.Asp2910Asp (chr7-5308283-G-A) – ACMG Classification: Benign (-15 pts)

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001080495.3(TNRC18):c.8730C>T(p.Asp2910Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 1,611,854 control chromosomes in the GnomAD database, including 22,717 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.14 ( 1641 hom., cov: 33)

Exomes 𝑓: 0.17 ( 21076 hom. )

Consequence

TNRC18
NM_001080495.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.44

Variant links:

Genes affected

TNRC18 (HGNC:11962): (trinucleotide repeat containing 18) Predicted to enable chromatin binding activity. Located in cytosol; mitochondrion; and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

TNRC18 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.55).

BP6

Variant 7-5308283-G-A is Benign according to our data. Variant chr7-5308283-G-A is described in ClinVar as [Benign]. Clinvar id is 1250212.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=1.44 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNRC18	NM_001080495.3 link	c.8730C>T	p.Asp2910Asp	synonymous_variant	Exon 30 of 30	ENST00000430969.6	NP_001073964.2	O15417-1A3KMH2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNRC18	ENST00000430969.6 link	c.8730C>T	p.Asp2910Asp	synonymous_variant	Exon 30 of 30	5	NM_001080495.3	ENSP00000395538.1		O15417-1
TNRC18	ENST00000399537.8 link	c.8730C>T	p.Asp2910Asp	synonymous_variant	Exon 30 of 30	5		ENSP00000382452.4		H9KVB4

Frequencies

GnomAD3 genomes

AF:

0.137

AC:

20858

AN:

152114

Hom.:

1641

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0659

Gnomad AMI

AF:

0.0482

Gnomad AMR

AF:

0.170

Gnomad ASJ

AF:

0.145

Gnomad EAS

AF:

0.104

Gnomad SAS

AF:

0.0930

Gnomad FIN

AF:

0.207

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.169

Gnomad OTH

AF:

0.134

GnomAD3 exomes

AF:

0.149

AC:

36288

AN:

244034

Hom.:

2928

AF XY:

0.148

AC XY:

19694

AN XY:

132694

show subpopulations

Gnomad AFR exome

AF:

0.0596

Gnomad AMR exome

AF:

0.163

Gnomad ASJ exome

AF:

0.134

Gnomad EAS exome

AF:

0.0943

Gnomad SAS exome

AF:

0.0921

Gnomad FIN exome

AF:

0.205

Gnomad NFE exome

AF:

0.171

Gnomad OTH exome

AF:

0.141

GnomAD4 exome

AF:

0.166

AC:

242268

AN:

1459622

Hom.:

21076

Cov.:

AF XY:

0.164

AC XY:

118844

AN XY:

725928

show subpopulations

Gnomad4 AFR exome

AF:

0.0581

Gnomad4 AMR exome

AF:

0.166

Gnomad4 ASJ exome

AF:

0.142

Gnomad4 EAS exome

AF:

0.102

Gnomad4 SAS exome

AF:

0.0946

Gnomad4 FIN exome

AF:

0.199

Gnomad4 NFE exome

AF:

0.177

Gnomad4 OTH exome

AF:

0.157

GnomAD4 genome

AF:

0.137

AC:

20853

AN:

152232

Hom.:

1641

Cov.:

AF XY:

0.139

AC XY:

10349

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.0658

Gnomad4 AMR

AF:

0.170

Gnomad4 ASJ

AF:

0.145

Gnomad4 EAS

AF:

0.105

Gnomad4 SAS

AF:

0.0935

Gnomad4 FIN

AF:

0.207

Gnomad4 NFE

AF:

0.169

Gnomad4 OTH

AF:

0.133

Alfa

AF:

0.153

Hom.:

961

Bravo

AF:

0.133

Asia WGS

AF:

0.0880

AC:

306

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

May 05, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

6.7

DANN

Benign

0.83

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.10

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over